New Galactic Order
by Psychic Werewolf Assassin
Summary: Conspiracy abound as Samus must rely on unlikely help to uncover the truth behind the Federation and its history. Reviews are appreciated.
1. Chapter 1

Disclaimer: Metroid is the sole property of Nintendo.

Chapter 1

On the fringes of Galactic Federation space was a Hunter-class gunship. It didn't directly enter the Federation's territory because it's owner, the infamous bounty hunter Samus Aran, was wanted for destroying the Federation's secretive bio-warfare lab hidden on the Biologic Space Labs. The station orbited the planet SR-388 before it was redirected into the planet after a parasitic organism simply called the X took it over and Samus wiped them out. Now the Federation labeled her as a terrorist simply because they couldn't let their citizens know what it was really about.

"Samus, a transmission is coming in." Her artificial intelligence, Adam, told her. The A.I. was actually her former commanding officer before his body was destroyed and his entire mind implanted into a computer.

"Patch it through, audio only." Samus replied, busy cleaning her Chozo Power Armor.

"Samus Aran, I'm a liason for the Federation to our freelance soldiers." A buzzy voice, like a bumble bee, spoke through the ship's speakers.

Samus brushed some strands of her blonde hair behind her ear. "I thought the Federation wanted my head."

"We do, unless you perform a mission for us. Then all charges against you will be dropped."

"And money?"

"I already told you the pay, your freedom."

"The job?"

"A small battalion of Space Pirates have been patrolling three adjacent systems on the edge of our space. I have sent the coordinates. Ridley is said to be among them. Kill him."

She blinked a few moments. "Ridley is dead. I saw his body crumble on the BSL."

"A simple clone Samus. It is unfortunate you had to destroy the labs, all our major genetic reasearch was there. Will you accept the job? If not, you can wait for your next chance of freedom, though it would be an indefinite wait."

"I'll do it."

"Splendid Samus, you don't know how much credits we save with hiring you."

Before she would let him continue, she cut the transmission. "I''ve got a bad feeling about this. Adam, set course for the closest of these sectors."

"Course set, engines ready. On your mark Lady."

"Mark."

* * *

"Commander, how was your trip?" The insectoid Pirate said.

"Fine. No difficulties here, were there?" A ten-foot tall, dark purple dragon replied.

"No Commander Ridley, all sensors are clear except for the asteroid belt, but we've doubled the probes there."

"Good. Keep me updated on all reports. I'll be heading for the fourth planet of this system alone. Abandon this frigate, take all munitions and supplies but leave it active after I'm gone."

"Why Commander?"

"The Huntress will be after us and I'm not losing the last few of our men in this region to her. I'll face her myself."

"Yes Commander."


	2. Chapter 2

Disclaimer: Metroid is the sole property of Nintendo.

Chapter 2

The planet's surface was pockmarked with artificial craters, deserts of sand were now of glass, oceans of what was once clean water were now acidic. Upon his perch of a broken crag, Ridley peered over the land and sighed mournfully. This world was once pleasent, the air used to be warm and sweet, wild animals hunting, plants and such were everywhere. He spread his wings and took off over the barren land, stopping at a valley with several caves. Ridley walked to the opening of the largest cavern.

"Nothing here's changed since then, has it?" He asked the darkness.

"Entering System 372, eight planets, the third, fourth, and fifth ones are habitable."

"Adam, active scan those three planets and their orbits."

"Pirate frigate, cloaked, orbiting the fourth planet. No life signs on-board."

"Take me in."

Samus cautiously peered around a corner, but not even the defenses were on. All the computers were purged except for a small few, including which planet Ridley had landed on. Her instincts screamed of a trap, but it was one she couldn't ignore. She tapped a few buttons on the control console and headed out.

After she was back on her ship, Samus uploaded all the information onto the ship's computer.

"Adam, set us up a landing sector on that planet down there."

"Course set. One biosign in the area, hard to tell if it's one that's large or very many, but scanners can't seem to find any other sign of multicellular life down there."

"Understood. Activate all weapons in case we need to chase him down."

He heard the subtle roar of the ship's engines and watched from the cave's mouth as it landed several kilometers away.

"A true Huntress must be ever vigilant for prey."


	3. Chapter 3

Disclaimer: Metroid is the sole property of Nintendo.

Chapter 3

It was worse then Zebes. The planet had no native life that which Adam could find. Her scanners kept her pointed in one direction, where he was bound to be at. The Federation had quarantined the planet because a catastrophe struck around twenty years ago. The craters and depressions looked man-made from the looks of the sand and dirt fused into glass from high temperatures.

"No sign of any civilization, but lots of conflict happened here."

He sat near the end of the cave, where it was most unstable. Ridley picked up a stone and rolled it around in his hand, small pearls of water forming at the edges of his eyes.

"I hate them, we all do. How they struck like cowards against us. You'll all rest well if I can finish this. If I can get her help"

Ridley lowered his head and closed his eyes.

The valley held many caves, but the largest one the bottom was her target. Her arm cannon raised, plasma setting set, Samus walked inside. She saw her foe sitting near the rear of the cave, his back turned to her, and raised to fire.

"Why do you hate me?"

The question took her by surprise. She expected him to attack and was ready for that, but not this. She shook her head.

"You destroyed my home."

"Did I? When and where was that?"

"Twenty years ago, planet K2-L."

Ridley sighed and turned his head so she could see an eye. "I was not yet old enough to really do anything. It was my father that led the attack." He said softly

"Everything I knew from then wiped out by the Space Pirates. And even years after that, you wiped out the Chozo, my adopted family. That's why I hate you." Samus spoke with great venom in her voice.

He was quiet for a few moments. "I hate the Federation, not you, but the Federation."

"And why is that?" She didn't care though, anything that could keep him off guard.

"The K2-L incident wasn't a justified operation, back then the Pirates suffered from communication problems. The group thought it was a special operations training center. Even now the Pirates have taught trainees about it and warned about the virtues of keeping the equipment in optimum performance."

"Just tell me before I blast you."

Ridley rose and turned to her. "This planet was my home twenty years ago. Like you, all I've known has been wiped out, but not from a communicaton problem. After K2-L, the Federation ordered the genocide of my species. We controlled the three systems here and lived in natural settings. The Pirates were our only source of technology and without them all of my people would be dead. The Federation bombarded many of us from space. I saw my mother, father, and all my siblings all vaporized by a single plasma blast."

Samus tightened her grip over her cannon. "That's a bullshit story."

"You've seen what the Federation does! When they found the Metroids, we feared they'd use them as bio weapons, so we conducted our own research. Each time we tried to stop their despotistic expasion, they'd send you in. Have you ever questioned what their orders were for? Have you ever thought for yourself?" He leered.

She gritted her teeth. "I was sent to kill you and that's what I'm going to do."

Ridley gave a sneer. "I've heard about the BSL incident and what the Federation said what happened. What were they doing there, more genetic weapons? And you needed to survive, so you destroyed it and then they branded you a terrorist. So what would they be paying you for my death? Your 'freedom'?"

"Why should you care?"

"Because if they aren't stopped this galaxy is going to hell in a handbasket. You can destroy me right here if you want, or you can help in our fight."

"So your Pirates can shoot me in the back? I don't think so." She raised her cannon and aimed for the ceiling above Ridely's head.

"It may not seem like much, but I give you my word. Besides, you've proven able to defeat many of our troops time and time again. If anything, we fear you'll shoot us in our backs."

They both remained silent and motionless for sometime. Then, slowly, Samus lowered her weapon.

"I don't like this, and I sure as hell don't trust you, but I'll help for as long as I see fit."

Ridley nodded. "Good. You don't have to come to our ships, you can recieve your orders from us via transmissions. Your first mission, lie to the Federation about my death and regain your freedom to travel. After that we'll be spreading files to certain people about the Federation's work in covert bio-reaserch and the attack on my people."

"I just want to ask, has anyone else beside you survived?"

"Yes. The Federation attacked our worlds one at a time so many did escape. We now live very far from Galatic space, near the galaxy edge."

She just nodded slowly.

"We must hurry. Only initiative will guarantee success."


	4. Chapter 4

Disclaimer: Metroid is the sole property of Nintendo.

Chapter 4

As Samus boarded her ship, an uneasy feeling entered her gut. She uploaded all information to Adam.

"Samus, I must be curious as to ask, why are you joining with the Pirates? It seems very out of character for you."

"I don't like it either, but maybe we can see which side's telling the truth when we get to the Federation capital."

"I am warning you that would be very unwise."

Samus ignored that. "I'm sure the liason left a frequency to contact him with."

"Yes he did."

"Call him."

A few mintues passed as Samus waited for the buzzy voice. It came through the ship speaker's.

"Yes?"

"Ridley's dead."

"So soon? Interesting. Did you face any problems, any Pirate activity along the way?"

"No, he forced them to flee so he could face me alone."

"And you survived, excellent work Samus. As promised all files about your terrorist act will be erased."

Before she could reply the transmission was cut off. With a sigh of impatience she ordered Adam to input the Federation's capital as her next designation.

"Get there quickly Adam, we don't have much time to waste."

"On it Lady."

* * *

"My calculations say she knows part of the truth. Do you think she suspects anything?" A cyborg asked

"Of course she does. Anyone with brains wouldn't ignore all the signs around them." The creature that replied was insectoid in appearance, with a sponge-like organ for a mouth and compound eyes. It's voice was buzzy, a very annoying buzz.

"There is a percentage she will be tracked and killed."

"By whom? No one can match her skills. The Federation special operatives are _taught_ about her accomplishments and many failed in similar situations. The end of the Federation is nigh and cannot be stopped."

"My calculations doubt they'll destroy the system of which the others run by, modify it perhaps, but to wipe it out would cause too much anarchy for them too handle."

"I do hope they find retribution. It was unfair after all."

"I agree that wiping so many out for the actions of one was illogical in the planning, but the virus did in fact work well."

"Is this meeting concluded? I must get back to work quickly to ensure her investigation is headed in the right direction."

"She must not be distracted the way they wish, she has her own resources to gauruntee that. That artificial intelligence you had constructed is one."

"Adam Malkovich is not an A.I., his person was completely infused into the computer."

"You must let me see this technology sometime in the future, as for now, I have certain contacts to talk with."

"As you wish."

* * *

"Commander, is it wise to have the Huntress work with us?"

"For a time. She'll have some to her own conclusions about our mission, but in the meantime she can be trusted."

"I do not like this Commander Ridley."

"It's the only way my friend."

"I understand Commander, but is the Huntress the only one that can assist us?"

"Yes. She has outsmarted us in the past and I believe she will become our greatest asset. Have the scanners been tested yet?"

"Yes Commander. They are working beyond expectation. We won't be caught off-guard by Federation antimatter bombs."

"And the shield technology?"

"Concussion and energy weapons are nullified, but EMP still shuts it down."

Ridley nodded. "Better then before. Try to strengthen them more though."

The Pirate bowed. "Right away Commander."


	5. Chapter 5

Disclaimer: Metroid is the sole property of Nintendo

Chapter 5

The Federation capital had pockets of industrial centers and large forests of residential areas. The military's major training academy was here as well. Her gunship registered for a landing zone near the Federation's archives. The request was filed away in the tangled mess of the Federation's mainframe, but it was instantly located, copied, and downloaded by an outside force.

Samus disembarked in civillian clothes with a datapad in her belt pouch. She walked the three blocks to the archives. It took her twenty standard minutes to search the archives for all information on the Space Pirates. Many sections were restricted for 'security' reasons and many more were censored, including some bits about a Federation fleet striking several large Pirate planets. With a few deft key strokes and plugging in her datapad, the firewalls fell apart and every last piece was downloaded. Quickly, she unplugged the pad and hurried out.

* * *

"So, she has downloaded all the information regarding the Pirates. Upload the information back in before the archivist notices it is missing." The cyborg ordered his fellows. "We can not afford the Federation to find any of this out."

* * *

Adam was intrigued by the mass of information Samus uploaded to her. He told her it would take him an hour to dissect everything if she didn't have him do anything else. She left him to his job and went to sleep in her cabin.

* * *

"I am hoping the shields we gave you are working adequetely." The insectoid said.

"They work better then expected, especially when you increase the power output." Ridley replied.

"But, the drain on your fusion reactors must prevent you from using other systems."

"Not at all. We still have plenty of Phazon. When used in a fusion reaction it gives us much more power then regular treatments. Our weapons and engines have also enjoyed the benefit from the upgrade. We still haven't been able to asses its half life, but it seems to take many years."

"Interesting Ridley. I'll be sure to let you keep this technology as your own."

Ridley gave a toothy grin. "The Pirates never wished to share this with you anyway. Both sides are upholding the deal so far, but we're not going to give more then we get."

"Nor did I expect you to Ridley. I spoke with Samus and she said she eliminated you. Seeing as you're still here I take it she's accepted your proposal. It's unfortunate we had to decieve her like this, but it is mild compared to what the Federation has done."

"When shall we tell her of what this is really about?"

"When she points that pretty cannon of hers towards our heads."

* * *

"This is amazing Samus. All our missions against the Pirates may not have been as legitimate as we thought. The Space Dragon Massacre was one such Federation mission. They really sent a fleet to wipe out an entire sapient species. Most of the Chozo eliminated was because of an engineered virus of unknown origin."

"Is it possible the files were planted?"

"No. The Federation archives are impossible to hack from outside the system. Files can be downloaded and restrictions removed only from direct access."

Samus frowned. "There has to be an angle we aren't seeing here. Someone has to be directing this."

"My analysis exactly. There can never just be two forces in a conflict like this. A third party must either be directing both sides or just influencing them."

"Head for Ridley's frigate. We need some more info."

"Course set Lady."


	6. Chapter 6

Disclaimer: Metroid is the sole property of Nintendo.

Chapter Six

The frigate docking bay had several Pirate technicians working at consoles. Samus stepped out of her ship in full gear, just in case. Many of the techies seemed frightened at her prescence.

"Where's Ridley?"

One pointed towards the map station. Samus uplinked into it and downloaded the whole frigate schematics. She proceeded throughout the ship's bulk, making her way. Pirates looked at her fearfully, like she was waiting for a reason to blast them to pieces.

Ridley was busy ordering several Pirates on the Command Deck. When he noticed Samus was there, he turned to face her.

"You didn't have to come on board Samus."

"What's my next assignment?"

"Another simple one. The Federation is transporting a cache of weapons to a military outpost. My soldiers are going to raid the envoy and acquire said weapons."

"Is your data reliable?"

"We are unsure. That is why you'll go on board the transport and report whether it's true or not."

"Why would I do that?"

Ridley glared. "Because the Federation is looking for guards with Pirate sightings near the sector they must traverse through."

"You want me to get aboard a convoy of Federation transports and transmit whatever info about them before the scheduled raid?"

"Precisely."

"When do I leave?"

"Right now would be best. The Federation hiring has been in effect for only a couple of hours and will end in a week."

Samus turned around. "What if your info's wrong?" She asked.

"Then contact us and we'll call off the raid." He replied.

She nodded slowly and left the Command Deck.

"Godspeed Samus." Ridley muttered under his breath.


	7. Chapter 7

Disclaimer: Metroid is the sole property of Nintendo.

Chapter Seven

Samus' Hunter-class gunship was swiftly approaching the desert/tropical world of Kerag 2. This world was home to the Dracon, a species of highly evolved and intelligent reptiles, but was poor with resources. It was also a main stop among space traders and was currently holding a shipment of unknown goods of the Federation.

She had already contacted the Federation governor for Kerag 2 and was welcomed as security for the convoy shipping out. She offered to escort from her own ship, but the governor wished her onboard in case any Pirates needed to be repelled.

Her inquiry to the captain as to what exactly was being transported was unsuccesful, for the moment. The ship's computer defenses feel easily to her hacking units. When the cargo manifest scrolled over her screen, she froze.

_No way...No fucking way!_ She thought, shocked. They weren't weapons like Ridley thought, nor food supplies. Embryos of various species were stored in cold conditions. Most of them had their DNA merged with other species, creating bastard creatures.

Shaken, Samus went to her room and contacted her ship.

"Yeah Lady?" Adam asked through the communication hub.

Before she started speaking, Samus checked the immediate system for monitoring units. Finding none, she uploaded the data to the A.I.

"...You have to be kidding me..." Adam said. "The Federation has been experimenting with gene manipulation, far before it even came into existence, but merging two different species _together_? That's...that's not right."

"Send all this information to Ridley immediately." She ordered. "Encrypted signal, highly concentrated so it cuts time."

"Aye aye Lady." He replied.

* * *

"Commander! Samus' report!" A Pirate said urgently. "It's been encrypted and sent from the convoy's current location!"

Ridley nodded and went to the computer. "How heavily encrypted is it?"

"Not so much. It'll take us a few moments." The computer beeped. "It's finished decoding."

He nodded. "Move aside." Ridley started reading the file.

_Commander,_

_The Federation's been experimenting in certain kinds of genetic manipulation. Such things include the actual fusion of two separated DNA strands to create embryos. Most of the subjects are human, with Space Pirate, Chozo, and even Space Dragon DNA merged into it._

Ridley read the rest of the report. "We strike now and capture the transport with these monsters. If the Federation loses them to us, they'll be mortified and we can see what they did."

The bridge crew acknowledged his orders and sent them to the other ships in the fleet. Within moments, the ships entered hyperspace and toward the convoy.


End file.
